MolNFT v1 · #137356 · protein
Engineered tryptophan synthase B-subunit from pyrococcus furiosus, PFTRPB2B9, with ser bound
5VM5 · Tryptophan synthase beta chain 1: “Engineered tryptophan synthase B-subunit from pyrococcus furiosus, PFTRPB2B9, with ser bound”. X-ray diffraction, 3 ligands (PLS, 0JO, NA), 17 pockets (best druggability 0.84). MolNFT v1 #137356 on…
- PDB
- 5VM5
- Type
- protein
- Length
- 1,532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase beta chain 1
- EC
- 4.2.1.20
- UniProt
- Q8U093
- Ligands
- PLS, 0JO, NA
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 384 | 48% helix, 21% strand | Q8U093 |
| B | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 382 | 48% helix, 20% strand | Q8U093 |
| C | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 383 | 47% helix, 20% strand | Q8U093 |
| D | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 383 | 49% helix, 20% strand | Q8U093 |
Ligands and binding sites
- PLS · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine · ligand · 3 copies · chains A, B, C
- 0JO · 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid · ligand · chains D
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.84 | 0.87 | 91 | NA |
| 2 | 149 | 0.82 | 0.98 | 36 | PLS |
| 3 | 148 | 0.81 | 0.98 | 36 | PLS |
| 4 | 158 | 0.80 | 0.96 | 35 | PLS |
| 5 | 124 | 0.80 | 0.98 | 36 | 0JO |
Interfaces
5 interfaces between chains.
- A–B · 1777 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1753 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 467 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 277 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 64 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VM5 · Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9, with Ser… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8U093 · AlphaFold monomer V2.0 prediction for tryptophan synthase beta chain 1 (Q8U093) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8U093
- Elsewhere: RCSB PDB 5VM5 · PDBe 5VM5 · UniProt Q8U093
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